Patient outcomes by baseline pathogen resistance phenotype and genotype in CERTAIN-1, a Phase 3 study of cefepime-taniborbactam versus meropenem in adults with complicated urinary tract infection

ABSTRACT CERTAIN-1 was a Phase 3, double-blind, randomized, parallel group study of the efficacy and safety of cefepime-taniborbactam versus meropenem in the treatment of adults with complicated urinary tract infection (cUTI), including acute pyelonephritis. We determined susceptibility of Enterobacterales and Pseudomonas aeruginosa baseline pathogens to cefepime-taniborbactam and comparators and characterized β-lactam resistance mechanisms. Microbiologic response and clinical response were assessed in patient subsets defined by baseline pathogens that were of cefepime-, multidrug-, or carbapenem-resistant phenotype or that carried β-lactamase genes. Among Enterobacterales baseline pathogens, 26.8%, 4.1%, and 3.0% carried genes for extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases, respectively. Within each treatment group, while composite success rates at Test of Cure in resistant subsets by pathogen species were similar to those by pathogen overall, composite success rates in meropenem patients were numerically lower for cefepime-resistant Escherichia coli (9/19; 47.4%) and ESBL E. coli (13/25; 52.0%) compared with E. coli overall (62/100; 62.0%). Cefepime-taniborbactam achieved composite success in 7/8 (87.5%) patients with carbapenem-resistant Enterobacterales and 8/9 (88.9%) patients with Enterobacterales with a carbapenemase gene (5 OXA-48-group; 2 KPC-3; 2 NDM-1). Cefepime-taniborbactam also achieved composite success in 8/16 (50.0%) patients and clinical success in 13/16 (81.3%) patients with P. aeruginosa; corresponding rates were 4/7 (57.1%) and 6/7 (85.7%) for meropenem. Cefepime-taniborbactam demonstrated efficacy in adult cUTI patients with cefepime-, multidrug-, and carbapenem-resistant pathogens including pathogens with ESBL, AmpC, and carbapenemase genes. CLINICAL TRIALS This study is registered with ClinicalTrials.gov as NCT03840148.

producing ESBLs, AmpC enzymes, serine carbapenemases, and NDM and VIM metallo-βlactamases (8)(9)(10)(11)(12).In the Phase 3 CERTAIN-1 cUTI study (13), cefepime-taniborbactam was superior to meropenem for the primary composite endpoint (microbiologic and clinical success) at Test of Cure (TOC) in the microbiologic Intent-to-Treat (microITT) population.We determined outcomes by pathogen resistance phenotype and geno type among patients in the CERTAIN-1 study, with a focus on the extended microITT population that included all patients in the microITT population plus patients with pathogens that were resistant to either cefepime-taniborbactam or meropenem.

Trial design and oversight
CERTAIN-1 was a randomized, double-blind, Phase 3 cUTI study.The primary objective was to evaluate the efficacy of cefepime-taniborbactam compared with meropenem in adult patients with cUTI, including acute pyelonephritis (AP).Details of trial design, oversight, eligibility criteria, and blinding have been previously reported (13).

Randomization and treatment
Patients were randomly assigned 2:1 to receive cefepime-taniborbactam 2 g/0.5 g intravenously every 8 h over 2 h or meropenem 1 g intravenously every 8 h over 30 min for 7 days (up to 14 days for patients with concurrent bacteremia).Oral step-down therapy was not permitted.

Identification and susceptibility testing of pathogens
Urine specimens were obtained at Screening, End of Therapy (EOT; within 24 h after the last dose of intravenous therapy), TOC (Day [19][20][21][22][23], and Late Follow-up (LFU; Day 28-35) visits for culture.Blood specimens were also collected at Screening and to document clearance.
Susceptibility testing of confirmed pathogens was performed centrally with concurrent quality control (13).Resistant phenotypes were based on Clinical and Laboratory Standards Institute (CLSI) breakpoints (14).Cefepime-taniborbactam MICs were interpreted with a provisional susceptible breakpoint of ≤16 µg/mL (12).An MDR phenotype corresponded to resistance to ≥1 agent in ≥3 classes of antibacterial agents.

Prespecified analysis population, end points, and efficacy assessments
The extended microITT population included all patients with a qualifying gram-negative uropathogen(s) at ≥10 5 CFU/mL, against which one or both study drugs had antibacterial activity [where activity was defined as a cefepime-taniborbactam MIC ≤16 µg/mL and a meropenem MIC ≤2 µg/mL (for Enterobacterales) or ≤4 µg/mL (for P. aeruginosa)], and no more than two microorganisms were identified regardless of colony count (13).
Microbiologic success required eradication of all baseline gram-negative uropatho gen(s) to <10 3 CFU/mL at TOC. Per-patient microbiologic response did not consider gram-positive pathogens.Gram-negative pathogens that were isolated at TOC were considered persistent for the present, prespecified analyses only if they matched the baseline pathogen clonal type, because isolation of a genotypically different pathogen at TOC indicated an infection by a distinct isolate compared with the baseline pathogen.Accordingly, patients with a uropathogen at ≥10 3 CFU/mL at TOC that was clonally unrelated to the baseline pathogen were assessed with a microbiologic response of eradication.Clonal relatedness was assessed by multilocus sequence typing (MLST) or, for Proteus mirabilis, pulsed field electrophoresis (PFGE).
Clinical success was defined as patient was alive, had symptomatic resolution or return to premorbid baseline of all core cUTI signs and symptoms, had no new core cUTI signs or symptoms, and had no use of additional antibacterial agents for cUTI.Composite success required both microbiologic and clinical success.
Assembled sequences were analyzed by proprietary software to align them against β-lactamase-encoding genes present in a curated database (15).AmpC gene variant and expression levels were determined for chromosomal ampC in Serratia spp.and Entero bacter spp., chromosomal bla PDC in P. aeruginosa, and plasmidic bla CMY in Klebsiella pneumoniae.Major porin gene sequences (among E. coli, Klebsiella spp., Enterobacter spp.and P. aeruginosa), efflux regulatory gene sequences (among P. aeruginosa), and the sequence of the ftsI gene encoding penicillin-binding protein 3 (PBP3; among E. coli and P. aeruginosa) were compared with reference alleles for qualifying isolates.
Post-baseline isolates with increases in study drug MIC of ≥4 fold compared with baseline were subjected to WGS analysis to assess potential resistance mechanisms.

Study population
The prespecified analyses reported here were performed in the extended microITT population (n = 452) that included all patients in the microITT population (n = 436) plus 16 patients with a baseline gram-negative uropathogen, against which only one study drug had an in vitro activity.The extended microITT population, therefore, included pathogens with diverse resistance profiles that were expected to be effectively treated by cefepime-taniborbactam and/or meropenem.
Plasmidic AmpC genes included CMY-4 (in three isolates of K. pneumoniae; all of which overexpressed the gene), CMY-2 (in one isolate of E. coli), and DHA-1/DHA-1-like (in two isolates of E. coli, and one isolate of S. marcescens).Intrinsic AmpC genes (AmpC type [ACT] variants in nine isolates of E. cloacae complex; CMY-70 in one isolate of C. freundii; and AmpC-like in one isolate of K. aerogenes; Table 2) were expressed at basal levels among characterized isolates.

Resistance profiles in baseline Enterobacterales and P. aeruginosa pathogens exclusive to the extended microITT population
In the subset of 16 patients in the extended microITT population that were excluded from the microITT population owing to resistance to one study drug, 3 patients (2 in the cefepime-taniborbactam group and 1 in the meropenem group) had baseline pathogens with cefepime-taniborbactam MICs of 32 µg/mL (meropenem MIC range, 1-2 µg/mL) and the remaining 13 patients (10 in the cefepime-taniborbactam group, 3 in the meropenem group) had pathogens that were resistant to meropenem (meropenem MIC range, 4->64 µg/mL; cefepime-taniborbactam MIC range, 0.12-16 µg/mL) (Table 3).All 16 baseline pathogens were MDR and 15/16 were resistant to cefepime.Among the cefepime-resistant pathogens, taniborbactam decreased the cefepime MIC by 16-fold against S. marcescens, by ≥32 fold against E. coli, by up to ≥2,048 fold against K. pneumoniae, and by up to ≥64 fold against P. aeruginosa.Overall, taniborbactam restored cefepime MICs to ≤16 µg/mL (provisionally Susceptible) for 13/15 of the cefepime-resist ant isolates.

Composite, microbiologic, and clinical outcomes by resistance phenotype and genotype
In the subset of 16 patients who were exclusive to the extended microITT popula tion, cefepime-taniborbactam demonstrated composite, microbiological, and/or clinical successes in patients with baseline pathogens having cefepime-taniborbactam MICs up to and including 32 µg/mL and meropenem MICs up to and including >64 µg/mL (Table 3).Eight of the 10 cefepime-taniborbactam-treated patients (80.0%) with meropenemresistant baseline pathogens achieved composite success whereas 9 (90.0%)achieved clinical success.Meropenem-treated patients achieved composite success in the three instances with meropenem-resistant pathogens.Furthermore, cefepime-taniborbactamtreated patients achieved composite success in 5/6 cases (83.3%) and clinical success in all six instances of patients with pathogens carrying serine carbapenemase genes (two isolates of K. pneumoniae with KPC-3, three isolates of K. pneumoniae with OXA-48, one isolate of K. pneumoniae with OXA-232) and in 3/3 patients (100%) with pathogens carrying metallo-β-lactamase genes (one K. pneumoniae, one S. marcescens each with NDM-1; one isolate of P. aeruginosa with VIM-2).Three patients (two in the cefepime-taniborbactam group, one in the meropenem group) had meropenem-susceptible baseline pathogens with cefepime-taniborbactam MICs of 32 µg/mL (Table 3).One of these cefepime-taniborbactam patients achieved composite success and the other was a composite non-responder whereas both achieved clinical success.The meropenem patient was not only a composite non-res ponder but also a microbiologic and clinical failure.
Within each treatment group of the extended microITT population overall, composite success rates at TOC in resistant subsets by pathogen species were generally similar to composite success rates by corresponding pathogen overall (Table S3).Two exceptions were in the meropenem group, where composite success rates were numerically lower Where there were 10 or more patients within each treatment group to permit between-group comparisons by resistance subset, composite and microbiologic success rates at TOC in the extended microITT population were numerically higher for cefepimetaniborbactam compared with meropenem for Enterobacterales overall, for E. coli overall, for cefepime-resistant, MDR, and ESBL E. coli, and for P. mirabilis overall (Table S3).Meropenem patients had numerically higher composite success rates in cefepime-resist ant, MDR, and ESBL subsets of K. pneumoniae.Clinical success rates across pathogens and resistance subsets were generally similar within and between treatment groups.
Cefepime-taniborbactam achieved composite success at TOC in 8/16 patients (50.0%) and clinical success in 13/16 patients (81.3%) with P. aeruginosa, respectively; corre sponding rates were 4/7 (57.1%) and 6/7 (85.7%) for meropenem (Table 3).Within each treatment group, success rates at TOC in patients with resistant isolates of P. aeruginosa were similar to those against P. aeruginosa overall; however, modest numbers of patients limited further interpretation.The one patient in the cefepime-taniborbactam group with P. aeruginosa carrying a metallo-β-lactamase (VIM-2) gene (Table 2; Table 3) achieved composite success at TOC.Other microbiologic outcomes are described in the supplemental material.

DISCUSSION
In the CERTAIN-1 study, substantial percentages of patients had baseline Enterobac terales pathogens in key resistance categories, consistent with the high burden of antimicrobial resistance globally (3,5,12,(17)(18)(19). Carriage of ESBL genes and an MDR phenotype were particularly prevalent in isolates of E. cloacae complex (47.1% and 64.7%, respectively) and K. pneumoniae (52.2% and 63.8%, respectively), reflecting the propensity of these organisms to acquire diverse resistance mechanisms.These observations, together with the finding that the most common uropathogen, E. coli, frequently carried ESBL genes or had an MDR phenotype underscore the need for active empiric and directed antibacterial agents for patients with cUTI.
Within each treatment group, rates of composite success at TOC in each resistance subset were generally similar to rates of composite success overall.However, mero penem composite success rates in patients with Enterobacterales overall and within the most prevalent resistance subsets of Enterobacterales were numerically lower than corresponding cefepime-taniborbactam composite success rates.Whether patient, microbiologic, or pharmacokinetic factors could explain numeric differences in rates of composite success at TOC between treatment groups for these patients, including the subset of patients with ESBL E. coli at baseline [cefepime-taniborbactam, 31/41 (75.6%); meropenem, 13/25 (52.0%)] remains to be determined.For example, it is unknown whether these lower composite response rates among meropenem patients could be attributed to differences in urinary pharmacokinetic parameters between the study drugs, as has been posited recently for tebipenem pivoxil compared with ertapenem (20,21).
Outcomes in patients with P. aeruginosa warrant particular attention as this gramnegative pathogen is frequently associated with nosocomial infections, treatment failures and antimicrobial resistance worldwide.In a recent global surveillance study, ceftazidime-avibactam and ceftolozane-tazobactam had in vitro activity against only 75% of carbapenemase-negative strains of CRPA, less than 50% of MDR P. aeruginosa strains, and <15% of carbapenemase-producing strains of CRPA (12).Hence, there is an unmet need for effective agents against resistant subsets of this challenging organism.Cefepime-taniborbactam at ≤16 µg/mL inhibited 4/4, 5/7, and 1/1 of these resistant P. aeruginosa strains, respectively, from patients in CERTAIN-1.These results, while limited, are consistent with corresponding percentages of 94.6%, 81.4%, and 62.2% against these resistant subsets, respectively, in global surveillance (12).
As also seen in other randomized controlled trials in adults with cUTI (20,(22)(23)(24)(25), clinical success rates in the CERTAIN-1 study were higher than microbiologic and composite (i.e., microbiologic plus clinical) success rates for both treatment groups.Whereas asymptomatic bacteriuria was associated with a higher rate of late clinical failure in a recent analysis of cUTI trial data (26), bacteriuria in the absence of clinical signs and symptoms has only modest sensitivity and poor positive predictive value as a biomarker for late clinical failure (27).Withholding antibiotic treatment for most patients with asymptomatic bacteriuria is consistent with current guidelines (28).
Efficacy analyses by pathogen and by resistance subset in the Phase 3 CERTAIN-1 study demonstrated that E. cloacae complex, E. coli, K. pneumoniae, P. aeruginosa, and P. mirabilis are appropriate target organisms for cefepime-taniborbactam treatment.Cefepime-taniborbactam may offer a potential new carbapenem-sparing treatment option for patients with cUTI due to cefepime-, multidrug-, and CRE and P. aeruginosa including pathogens with ESBL, AmpC, and carbapenemase genes that have become commonplace worldwide.

TABLE 1
Susceptibility summary for baseline isolates of Enterobacterales and P. aeruginosa (extended MicroITT population) f

MIC 90 or MIC range (µg/mL); % Susceptible Pathogen phenotype/genotype (n; % of total) a Cefepime Cefepime-tanibor bactam b
Underlined values correspond to the percentage of isolates in each phenotypic or genotypic subset that are susceptible to the given agent.
(12)tients had at least one gram-negative uropathogen at baseline and not more than two uropathogens in total.bIn the absence of breakpoints for cefepime-taniborbactam, % Susceptible corresponds to the percentage of isolates inhibited at ≤16 µg/mL(12).c Resistance to ≥1 agent in ≥3 classes of antibacterial agents.d Includes pathogens carrying plasmidic ampC and pathogens at high risk of clinically significant AmpC production due to an inducible ampC gene (E.cloacae complex, Klebsiella aerogenes, and Citrobacter freundii; 7).e Meropenem-vaborbactam MICs against P. aeruginosa were interpreted using the EUCAST susceptible breakpoint of ≤8 µg/mL.f g Abbreviation: ESBL, extended spectrum β-lactamase genotype.Full-Length Text Antimicrobial Agents and Chemotherapy July 2024 Volume 68 Issue 7 10.1128/aac.00236-244

TABLE 2
Summary of β-lactamase gene content and cefepime, cefepime-taniborbactam, and meropenem MICs for characterized baseline isolates of Enterobacterales and P. aeruginosa (extended microITT population) (Continued on next page)

TABLE 3
Phenotypic and genotypic profiles of baseline pathogens, and composite, microbiologic, and clinical outcomes at TOC, for patients in the extended microITT population and excluded from the microITT population, by treatment group f, g MICs were interpreted using proposed breakpoints of Susceptible ≤16 µg/mL, Resistant ≥32 µg/mL based on 12. Rows are ordered from lowest to highest MIC to study drug received in the corresponding treatment group.patients with cefepime-resistant E. coli (9/19; 47.4%) and ESBL E. coli (13/25; 52.0%) compared with E. coli overall (62/100; 62.0%).